##Identifying reversal genes

##Looking for common reversal genes

## Loading required package: grid
## Loading required package: futile.logger

##The 19 common genes:

##Cyp4p1; Cytochrome P450 4p1; May be involved in the metabolism of insect hormones and in the breakdown of synthetic insecticides.

##CG13962; Unknown function

##Cpr51A; Cuticular protein 51A; Predicted to be a structural constituent of chitin-based larval cuticle. Involved in sexual reproduction. Located in extracellular space.

##CG11438; Predicted to enable phosphatidate phosphatase activity. Predicted to be involved in phospholipid dephosphorylation; phospholipid metabolic process; and signal transduction. Predicted to be active in plasma membrane.

##Sgs5bis; Predicted to be involved in puparial adhesion. Predicted to be located in adhesive extracellular matrix.

##sad; shadow; shadow (sad) encodes a cytochrome P450 involved in ecdysteroid biosynthesis. It shows a mitochondrial localization and catalyzes the addition of a hydroxyl group to the 2 carbon of the cholesterol ring. sad mutants fail to undergo head involution, dorsal closure or to secrete cuticle.

##Lip2; Lipase 2; Predicted to enable triglyceride lipase activity. Predicted to be involved in lipid metabolic process. Human ortholog(s) of this gene implicated in Wolman disease; autosomal recessive congenital ichthyosis 8; and cholesterol ester storage disease.

##CG4757; Enables serine hydrolase activity. Is expressed in adult head. Human ortholog(s) of this gene implicated in colorectal cancer and gastrointestinal system cancer.

##CG14229; Is expressed in organism.

##CG15406; Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be active in membrane.

##CG3270; Predicted to be involved in mitochondrial respiratory chain complex I assembly. Predicted to be active in cytoplasm. Is expressed in adult head. Human ortholog(s) of this gene implicated in nuclear type mitochondrial complex I deficiency 19.

##CG9877; Unknown function

##CG13905; mat; materazzi; Enables lipid binding activity. Is expressed in adult head.

##Zip71B; Zinc/iron regulated transporter-related protein 71B; Zinc/iron regulated transporter-related protein 71B (Zip71B) encodes a protein involved in zinc detoxification and zinc transmembrane import.

##CG17027; Predicted to enable inositol monophosphate 1-phosphatase activity. Predicted to be involved in inositol metabolic process and signal transduction. Predicted to be located in cytoplasm. Is expressed in embryonic Malpighian tubule and embryonic proventriculus.

##nom; numerous disordered muscles; Enables DNA binding activity. Involved in larval somatic muscle development. Predicted to be located in nucleus. Is expressed in embryonic/larval fat body; organism; and ring gland primordium.

##CG16727; Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in membrane. Orthologous to human SLC22A24

##CG9702; Predicted to enable sulfate transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in membrane. Predicted to be active in plasma membrane. Is expressed in adult head. Orthologous to human SLC26A11

##CG43740; Located in nucleoplasm. Is expressed in adult brain cell body rind.

##Total Response Genes in Silent-Rescue vs Silent

##Overlap in Total Response Genes in Silent-Rescue vs Silent

##Genes that are Reversal Genes in the “Silent-Rescue vs Silent” ##Reversal genes that normally respond to the rescue

##Identifying reversal genes that are also sDEG in WT ‘rescue’ condition

###Grey points should indicate a ‘conserved response gene’. That is G85R-rescue with FC similar to the obeserved FC in WT-rescue. Same direction and similar magnitude (within 50% of FC). ##Red and Blue indicates Reversal genes that are not following a ‘conserved response gene’ ##Gold are any ‘conserved response genes’ that are sDEG in WT Rescue ##Pink and Cyan are any Reversal genes that are not ‘conserved response’ but are sDEG in WT response

##Assessing the number of Conserved Response genes in the Reversal Genes

##Distinguishing Conserved Response genes between control DEGs and control sDEGs

##Conserved Reversal Genes

##Can be sDEG or not in Control response

##Common conserved reversal genes

##Is in all groups

##Cpr51A; Cuticular protein 51A; Predicted to be a structural constituent of chitin-based larval cuticle. Involved in sexual reproduction. Located in extracellular space.

##Is in male and female Df but not OE

##vir-1; virus-induced RNA 1; virus-induced RNA 1 (vir-1) is produced from a promoter that is induced by viral infection. It can be used as a marker of the induction of an antiviral response. Its expression is regulated by the Jak/STAT pathway.

##CG34136; Unknown function

##Reversal Metabolite analysis